e70152e44cc66cc599ff6b699eb8adc07f3e656a
kent
  Sat May 24 21:09:34 2014 -0700
Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
diff --git src/hg/inc/featureBits.h src/hg/inc/featureBits.h
index 1b618db..a5690ac 100644
--- src/hg/inc/featureBits.h
+++ src/hg/inc/featureBits.h
@@ -1,92 +1,95 @@
 /* FeatureBits - convert features tables to bitmaps. */
+
+/* Copyright (C) 2008 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
 #ifndef FEATUREBITS_H
 #define FEATUREBITS_H
 
 #ifndef BITS_H
 #include "bits.h"
 #endif
 #include "hdb.h"
 #include "cart.h"
 #include "bed.h"
 
 struct featureBits
 /* A part of a sequence. */
     {
     struct featureBits *next;
     char *name;		/* Symbolic name for feature. */
     char *chrom;	/* Chromosome name. */
     int start, end;	/* Start/end half open zero based. */
     char strand;	/* + or - or ? */
     };
 
 void featureBitsFree(struct featureBits **pBits);
 /* Free up feature bits. */
 
 void featureBitsFreeList(struct featureBits **pList);
 /* Free up a list of featureBits */
 
 struct featureBits *fbGetRange(char *db, char *trackQualifier, char *chrom,
                                int chromStart, int chromEnd);
 /* Get features in range. */
 
 struct featureBits *fbGetRangeQuery(char *db, char *trackQualifier,
 	char *chrom, int chromStart, int chromEnd, char *sqlConstraints,
 	boolean clipToWindow, boolean filterOutNoUTR);
 /* Get features in range that match sqlConstraints. */
 
 boolean fbUnderstandTrack(char *db, char *track);
 /* Return TRUE if can turn track into a set of ranges or bits. */
 
 void fbOrBits(Bits *bits, int bitSize, struct featureBits *fbList,
 	int bitOffset);
 /* Or in bits.   Bits should have bitSize bits.  */
 
 void fbOrTableBits(char *db, Bits *bits, char *trackQualifier, char *chrom, 
 	int chromSize, struct sqlConnection *conn);
 /* Ors in features in track on chromosome into bits.  */
 
 void fbOrTableBitsQueryMinSize(char *db, Bits *bits, char *trackQualifier, char *chrom, 
         int chromSize, struct sqlConnection *conn, char *sqlConstraints,
 	boolean clipToWindow, boolean filterOutNoUTR, int minSize);
 /* Ors in features matching sqlConstraints in track on chromosome into bits. 
    Skips featureBits that are less than minSize. minSize is useful for introns where
    things less than a given threshold are alignment gaps rather than introns. */
 
 void fbOrTableBitsQuery(char *db, Bits *bits, char *trackQualifier, char *chrom, 
 	int chromSize, struct sqlConnection *conn, char *sqlConstraints,
 	boolean clipToWindow, boolean filterOutNoUTR);
 /* Ors in features matching sqlConstraints in track on chromosome into bits. */
 
 
 
 void fbOptions(char *db, char *track);
 /* Print out an HTML table with radio buttons for featureBits options. */
 
 void fbOptionsHti(struct hTableInfo *hti);
 /* Print out an HTML table with radio buttons for featureBits options.
  * Use defaults from CGI. */
 
 void fbOptionsHtiCart(struct hTableInfo *hti, struct cart *cart);
 /* Print out an HTML table with radio buttons for featureBits options. 
  * Use defaults from CGI and cart. */
 
 char *fbOptionsToQualifier();
 /* Translate CGI variable created by fbOptions() to a featureBits qualifier. */
 
 struct featureBits *fbFromBed(char *db, char *trackQualifier, struct hTableInfo *hti,
 	struct bed *bedList, int chromStart, int chromEnd,
 	boolean clipToWindow, boolean filterOutNoUTR);
 /* Translate a list of bed items into featureBits. */
 
 struct bed *fbToBedOne(struct featureBits *fb);
 /* Translate a featureBits item into (scoreless) bed 6. */
 
 struct bed *fbToBed(struct featureBits *fbList);
 /* Translate a list of featureBits items into (scoreless) bed 6. */
 
 void bitsToBed(char *db, Bits *bits, char *chrom, int chromSize, FILE *bed, FILE *fa, 
 	       int minSize);
 /* Write out runs of bits of at least minSize as items in a bed file. */
 
 #endif /* FEATUREBITS_H */